7-107713909-GTATTATTATTAT-GTATTATTAT

Variant names:

• chr7-107713909-GTAT-G
• rs34694220
• NM_000441.2:c.2319+1307_2319+1309delATT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000441.2(SLC26A4):​c.2319+1307_2319+1309delATT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (19828 hom., cov: 0)
• Consequence: SLC26A4 NM_000441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

Genes affected

SLC26A4 (HGNC:8818): (solute carrier family 26 member 4) Mutations in this gene are associated with Pendred syndrome, the most common form of syndromic deafness, an autosomal-recessive disease. It is highly homologous to the SLC26A3 gene; they have similar genomic structures and this gene is located 3' of the SLC26A3 gene. The encoded protein has homology to sulfate transporters. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC26A4	NM_000441.2	c.2319+1307_2319+1309delATT		intron_variant	Intron 20 of 20	ENST00000644269.2	NP_000432.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC26A4	ENST00000644269.2	c.2319+1288_2319+1290delTAT		intron_variant	Intron 20 of 20		NM_000441.2	ENSP00000494017.1
SLC26A4	ENST00000492030.2	n.505+1288_505+1290delTAT		intron_variant	Intron 5 of 5	5
SLC26A4	ENST00000644846.1	n.*221+1288_*221+1290delTAT		intron_variant	Intron 9 of 9			ENSP00000494344.1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 75761 AN: 148788 Hom.: 19821 Cov.: 0

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.498

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.509 AC: 75797 AN: 148868 Hom.: 19828 Cov.: 0 AF XY: 0.508 AC XY: 36861 AN XY: 72538

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.495

Bravo AF: 0.520

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34694220; hg19: chr7-107354354;